Find Missing SDS

This program is designed specifically for Open Enventory to fix issue with molecule missing sds (could not be extracted through "Read data from supplier") This programs does:

GitHub - khoivan88/oe_find_sds-public: for Open Enventory, this script is used to find missing SDS for molecule in your existing Open Enventory databaseGitHub

DETAILS

This programs does:

1. Connect into mysql database and find molecule in 'molecule' table of specific database and find those molecule with missing sds

2. Try to download sds files into a folder in /var/lib/mysql/missing_sds

3. Update those sql entries with new downloaded sds files

REQUIREMENTS

• root access to the server hosting Open Enventory

• Python 3+

• This file is made for Linux environment, you should be able

  to used it on other OS with changing the location of the "download_path"

USAGE

After cloning this repo onto the Open Enventory server:

1. Change into directory of the new file:

   cd find_missing_sds-public

2. (Optional): create virtual environment for python to install dependency:

   # you can change "find_missing_sds_venv" to another name too
   python3 -m venv find_missing_sds_venv   # Create virtual environment
   source find_missing_sds_venv/bin/activate    # Activate the virtual environment

3. Install python dependencies:

   pip install -r requirements.txt

4. Run the program:

   # Replace "find_missing_sds_v5" with latest version if neccessary
   python3 find_missing_sds_v5/find_missing_sds.py

   • Answer questions for:

     • confirming running under root

     • mySQL root password (typing password will not be shown on screen)

     • the name of the database you want to update (twice to confirm)

VERSIONS

Version 5:

• Incorporated result from Fluorochem

• Fixing bug with existing default_safety_sheet_url and default_safety_sheet_mime

  by setting them to NULL

Version 4:

• Testing using cheminfo.org/webservices by extracting catalog number from fluorochem

Version 3:

• Refactor extracting url download into its own method

• Add extracting url download from chemicalsafety.com

Version 2:

• Add asking if user is root and password

• Add asking what database to be modified

• Switch to extracting data from https://www.fishersci.com because Chemexper

  has limited requests